1000 Genomes Project - what have been done so far
A2 Variant Calling
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Allele specific alternative splicing
Allele specific expression
Allelic mapping bias
Alternative soft-splicing analysis
Alternative splicing analysis
Analysis
Analysis group
Analysis group 2011 January 12
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Analysis group 2012 April 5
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Analysis group 2012 August 9
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Analysis group 2012 January 12
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Analysis group 2012 May 3
Analysis group 2012 October 11
Analysis group 2012 October 18
Analysis group 2012 October 25
Analysis group 2012 October 4
Analysis group 2012 September 13
Analysis group 2012 September 20
Analysis group 2012 September 27
Analysis plan
Background
Barcelona July 2012
Basic methodology
Basic miRNA analyses
Category
Category:RNA
Category:WP4: RNAseq
Cats
Cell lines
Contribution of alternative splicing on the between-population transcript variability
Contribution of alternative splicing on the transcript variability
DNA contamination
Data storage
Differential Expression
Differential isoform usage
EBV contamination
EGA
ENA / Arrayexpress
EQTL
Epstein-Barr virus activity
Exon quantification
Expression level covariates
FTP
FTP file upload instructions
File:13 09 2012 Geuvadis splicing.pptx
File:20 09 2012 Geuvadis splicing.pptx
File:2012 08 23 mbarann soft splicing.pptx
File:2012-04-16 Geuvadis Analysis CNAG Micha.pptx
File:2012-04-16 Geuvadis Analysis CRG Jean.pdf
File:2012-04-16 Geuvadis Analysis CRG Marc.pptx
File:2012-04-16 Geuvadis Analysis EBI Natalja.pdf
File:2012-04-16 Geuvadis Analysis HMGU Thomas W.ppt
File:2012-04-16 Geuvadis Analysis Intro Tuuli.pptx
File:2012-04-16 Geuvadis Analysis Kiel Rob.pptx
File:2012-04-16 Geuvadis Analysis LUMC Peter.pptx
File:2012-04-16 Geuvadis Analysis Oxford Manuel.pptx
File:2012-04-16 Geuvadis Analysis Programme.docx
File:2012-04-16 Geuvadis Analysis UNIGE Tuuli.pptx
File:2012-04-16 Geuvadis Analysis UU Olof.pdf
File:2012-04-17 Geuvadis Analysis Action Plan Tuuli.pptx
File:2012-04-30 MS Gene-Discovery.png
File:2012-04-30 MS known RNA-edits.png
File:2012-07-09 GEUVADIS RNA EBI Mar.pdf
File:2012-07-09 GEUVADIS RNA IKMB Philip.pptx
File:2012-07-09 GEUVADIS RNA Oxford Manny.pdf
File:2012-07-09 GEUVADIS RNA UNIGE Tuuli.pptx
File:2012-07-09 GEUVADIS RNA UU Olof.ppt
File:2012-07-09 GEUVADIS RNA basics Tuuli.pptx
File:2012-07-10 GEUVADIS LUMC Irina.pdf
File:2012-07-10 GEUVADIS RNA CRG Jean.pdf
File:2012-07-10 GEUVADIS RNA CRG Marc.pptx
File:2012-07-10 GEUVADIS RNA EBI Natalja.pdf
File:2012-07-10 GEUVADIS RNA HMGU Thomas.ppt
File:2012-07-10 GEUVADIS RNApaper notes.pptx
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-03 16-18-12.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-04 11-10-16.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-05 09-10-51.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-05 15-53-52.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-07 11-29-43.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-11 08-31-26.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-11 09-15-16.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-11 10-10-53.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-11 10-57-46.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-11 16-12-51.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-13 08-28-00.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-13 09-04-53.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-13 14-03-41.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-13 14-47-32.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-13 15-27-45.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-13 16-09-15.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-14 08-38-21.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-17 16-00-49.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-17 16-30-59.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-18 08-31-32.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-18 09-01-17.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-18 10-46-00.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-18 11-41-52.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-18 15-40-19.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-19 13-52-25.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-19 14-20-54.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-19 15-26-33.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-21 14-31-31.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-21 15-13-58.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-21 15-41-55.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-24 08-27-50.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-24 09-10-05.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-24 09-58-34.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-24 10-36-12.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-24 12-14-15.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-24 13-51-17.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-24 14-28-01.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-24 15-00-34.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-24 15-35-22.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-24 16-03-45.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-24 16-37-43.pdf
File:2100 expert Eukaryote Total RNA Nano DE04105537 2011-10-26 16-15-37.pdf
File:2100 expert High Sensitivity DNA Assay DE04105537 2011-11-24 11-40-38.pdf
File:ASAS.png
File:ASHG abstract Tuuli.docx
File:ASHG2012 poster Lappalainen.pdf
File:Admintestimage.png
File:Agilent RNA 6000 Nano kit guide.pdf
File:Allvariants plots new.png
File:Allvariants plots.pdf
File:Allvariants plots.png
File:AllvsFiltered.jpg
File:AnalysisTestSamples Marc.pdf
File:Asas 11 10.pdf
File:Asas462 counts props.png
File:Asasp005 ase pdistr.png
File:Ase 06 2012.pdf
File:Ase bas stat scatter.png
File:Ase basiccounts hist.png
File:Ase dist lab boxplot.png
File:Ase dist pop boxplot.png
File:Ase effectsize fr.462.40sampled.p001 smoothscatter.png
File:Ase mds labcol.png
File:Ase mds popcol.png
File:Ase stats all Page 1.png
File:Ase stats ind plot1.png
File:Ase stats tot 18.pdf
File:Ase stats totsites Page 1.png
File:Ase stats totsites Page 2.png
File:CEU p30 test.png
File:CEU-vls-sum.png
File:CSHL abstract.docx
File:CSHL2012 poster Lappalainen.pdf
File:Cellbanks samplelist.xlsx
File:Classes of splice-site variants.PDF
File:Collaboration.jpg
File:D stat hist.pdf
File:D stat hist.png
File:Datafull pca1 8.pdf
File:Datafull pca1 8.png
File:Differences boxplot.png
File:Diffexpression psi.pdf
File:Disc ind cumdiff indlines means.png
File:Dstats raw lab pop boxplot.png
File:Ebv cor.png
File:Ebv cov ranks.png
File:Ebv hist.png
File:Ebv volcano.png
File:Example.pdf
File:Example.png
File:Exon cisgenes eur exon 6 8.png
File:Exon cisgenes yri exon 6 8.png
File:Exon tr quantification covariate correlation.xlsx
File:Exon462.png
File:ExonJunc.png
File:Fig AAF.png
File:Fig psi worse neutral.png
File:Figure1.pdf
File:Figure2.pdf
File:Figure3.pdf
File:Figure4.pdf
File:GV-2012-09-20 sammeth.pdf
File:GV-2012-10-11 Splicing.pdf
File:Gem bam comparison.pdf
File:Gene Activity.GIF
File:Gene Discovery.PNG
File:Gene discovery final.pdf
File:Genediscovery.pdf
File:Genediscovery.png
File:General-nei-gencv12-01RPKM-GBR.pdf
File:Geu-dMean-CEUFIN.png
File:Geu-dMean-CEUYRI.png
File:Geu-dMean-CEUcomp.png
File:Geu-dMean-MedianComp-diffRatios.png
File:Geu-dMean-MedianComp.png
File:Geu-dMean-YRIcomp.png
File:Geu-disp-popSpec-disp.png
File:Geu-disp-popSpec-nbiso.png
File:Geu-disp-popSpec-vls.png
File:Geu-disp-venn-spec.png
File:Geu-disp-venn.png
File:Geu-geneExprSplicing-CEUvsFIN.pdf
File:Geu-geneExpressionContribution-GBR.pdf
File:Geu-geneExpressionContributionBtwPopulation.pdf
File:Geu-majIsoRatio-GBR.pdf
File:Geu-majorIsoRatio-CEU.png
File:Geu-majorIsoRatio-FIN.png
File:Geu-majorIsoRatio-GBR.png
File:Geu-majorIsoRatio-TSI.png
File:Geu-majorIsoRatio-YRI.png
File:Geu-nbExpIso-CEU.png
File:Geu-nbExpIso-CEUvsFIN.png
File:Geu-nbExpIso-FIN.png
File:Geu-nbExpIso-FINvsYRI.png
File:Geu-nbExpIso-GBR.png
File:Geu-nbExpIso-GBRvsTSI.png
File:Geu-nbExpIso-TSI.png
File:Geu-nbExpIso-YRI.png
File:Geu-nbIso-GBR.pdf
File:Geu-ratio-popSpec-nbiso.png
File:Geu-ratio-popSpec-vls.png
File:Geu-ratio-venn-spec.png
File:Geu-ratio-venn.png
File:Geu-shannonEntropy-GBR.pdf
File:Geu-splEntropy-CEU.png
File:Geu-splEntropy-FIN.png
File:Geu-splEntropy-GBR.png
File:Geu-splEntropy-TSI.png
File:Geu-splEntropy-YRI.png
File:Geu-totalIsoExpr-CEUvsFIN.pdf
File:Geu-vls-5pop-Vls2Vt.png
File:Geu-vls-5pop-VlsVt.png
File:Geu-vls-CEU-GEnoise-density.png
File:Geu-vls-CEU-GEnoise.png
File:Geu-vls-CEU-sum.png
File:Geu-vls-CEU-vlsvt.png
File:Geu-vls-CEUvsFIN-vlsvr.png
File:Geu-vls-FIN-sum.png
File:Geu-vls-GBR-sum.png
File:Geu-vls-TSI-sum.png
File:Geu-vls-YRI-sum.png
File:Geu-vlsvt-CEUFIN.png
File:Geu-vlsvt-CEUGBR.png
File:Geu-vlsvt-CEUYRI.png
File:Geu-vlsvt-FINGBR.png
File:Geuvadis eqtl methods.pdf
File:Geuvadis samplesheet mRNA CRG.xlsx
File:Geuvadis samplesheet mRNA HMGU.xlsx
File:Geuvadis samplesheet mRNA ICMB.xlsx
File:Geuvadis samplesheet mRNA LUMC.xlsx
File:Geuvadis samplesheet mRNA MPIMG.xlsx
File:Geuvadis samplesheet mRNA UNIGE updated.xlsx
File:Geuvadis samplesheet mRNA UNIGE.xlsx
File:Geuvadis samplesheet mRNA UU.xlsx
File:Geuvadis samplesheet miRNA CRG.xlsx
File:Geuvadis samplesheet miRNA HMGU.xlsx
File:Geuvadis samplesheet miRNA ICMB submission2.xlsx
File:Geuvadis samplesheet miRNA ICMB.xlsx
File:Geuvadis samplesheet miRNA LUMC.xlsx
File:Geuvadis samplesheet miRNA MPIMG.xlsx
File:Geuvadis samplesheet miRNA UNIGE.xlsx
File:Geuvadis samplesheet miRNA UU.xlsx
File:Geuvadis-logo.png
File:IMG 8450.JPG
File:IMG 8461.JPG
File:IMG 8464.JPG
File:IMG 8465.JPG
File:Ibs mds scatter k1 2.pdf
File:Ibs mds scatter k1 2.png
File:Integratedanalysis.pdf
File:Intron462.png
File:Junction cisgenes eur 6 8.png
File:Junction cisgenes yri 6 8.png
File:Junction462.png
File:Lab effects Spearman vs OPS Pearson filtered data.jpg
File:Lab seqstat correlations scatter.pdf
File:Lappalainen CoverLetter.pdf
File:Lappalainen Main text.docx
File:Lappalainen Supplementary Material.pdf
File:Lappalainen Supplementary Tables 4-6.xlsx
File:Lofupdate24052012.pdf
File:Main Figures Tables.pptx
File:Mapping stats.png
File:Mb soft splicing graph1.pdf
File:Mb soft splicing graph1.png
File:Mb soft splicing graph10.png
File:Mb soft splicing graph11.png
File:Mb soft splicing graph12.png
File:Mb soft splicing graph13.png
File:Mb soft splicing graph14.png
File:Mb soft splicing graph15.png
File:Mb soft splicing graph16.png
File:Mb soft splicing graph17.png
File:Mb soft splicing graph18.png
File:Mb soft splicing graph19.png
File:Mb soft splicing graph2.png
File:Mb soft splicing graph3.png
File:Mb soft splicing graph4.png
File:Mb soft splicing graph5.png
File:Mb soft splicing graph6.png
File:Mb soft splicing graph7.png
File:Mb soft splicing graph8.png
File:Mb soft splicing graph9.png
File:Mirna cisgenes eur 6 8.png
File:Mirna452.png
File:One vs all fc2.jpg
File:One vs all fc3.jpg
File:PEER K covariate correlation.xlsx
File:Paper outline 09.docx
File:Pca all pc1 2.png
File:Pca eur pc1 3.png
File:Pca yri pc1 2.png
File:Pedro DEG popspecific.pdf
File:Pedro PSI std0.15.pdf
File:Peer venns.png
File:Proportions boxplots.pdf
File:QC Tuuli 07 2012.pdf
File:Qc boxplots.pdf
File:Qqplot fullaxis.png
File:Qqplot sep fullaxis.png
File:Quality by position lineplots.pdf
File:Qubit manual.pdf
File:README UNIGE bam submission1.txt
File:README UNIGE submission1.txt
File:Random example.png
File:Raw dstat filt hist mirna.png
File:Raw dstat hist mirna.png
File:Raw dstat hist.png
File:Raw rho hist.png
File:Raw rho mds labcolor mirna.png
File:Raw rho mds popcolor mirna.png
File:Rawres dstat exclNA19144 hist.pdf
File:Readcount hists.png
File:Ref nonref ratio boxplot.pdf
File:Ref nonref ratio boxplot.png
File:Repeat462.png
File:Repl corr mrna mirna.png
File:Replicate ratio scatters.png
File:Replicate ratiodiff sigs coverage scatter.png
File:Replicate rho part boxplot.png
File:Replicate rho part lab sample boxplot.png
File:Rhoscatter 480 pop lab.png
File:Rhoscatter 660 pop lab.png
File:Rhoscatter repl pop lab mirna.png
File:Rhoscatter repl pop lab mrna.png
File:Rin correlations scatter.pdf
File:Rin qual.pdf
File:SQTL-ATP5SL-snp 19 41937095.png
File:SQTL-ERAP2-snp 5 96244549.png
File:SQTL-IRF5-snp 7 128573967.png
File:SQTL-classEvent-CEU.png
File:SQTL-classEvent-FIN.png
File:SQTL-classEvent-GBR.png
File:SQTL-classEvent-TSI.png
File:SQTL-classEvent-YRI.png
File:SQTL-classEvent.png
File:SQTL-gwas-immune-prop-CEU.png
File:SQTL-gwas-immune-prop-FIN.png
File:SQTL-gwas-immune-prop-GBR.png
File:SQTL-gwas-immune-prop-TSI.png
File:SQTL-gwas-immune-prop-YRI.png
File:SQTL-rk30PopShare.png
File:SQTL-rkPopShare.png
File:SQTL-sigPopShare.png
File:Sample bioanalyzerdate.txt
File:Sandbox5 pca12.png
File:Seq protocol summary 111114updated.docx
File:Seq protocol summary 120229updated.docx
File:Seq protocol summary.docx
File:Snp example.png
File:Splice-site variants.png
File:SpliceGeuvadisRivas27092012.pdf
File:Splicevar example.png
File:Stdsup0.15.png
File:Stdsup0.2.png
File:Summary list 121012.txt
File:Suppl Figures Tables.pptx
File:TC - QC - Uppsala.pdf
File:TC Minutes WP4 2011 05 06.docx
File:TC Minutes WP4 2011 09 16.docx
File:TC Minutes WP4 2011 11 03.docx
File:Test pdf.PDF
File:Tr cisgenes eur tr 5 6 8.png
File:Tr462.png
File:Trizol reagent.pdf
File:VarCont-5pop-BwVar.png
File:VarCont-5pop-GeBwVar.png
File:VarCont-5pop-diffGenes-bp.png
File:VarCont-5pop-rand-bp.png
File:VarCont-CEUvsGBR-BwVar.png
File:VarCont-CEUvsGBR-GeBwVar.png
File:VarCont-CEUvsYRI-BwVar.png
File:VarCont-CEUvsYRI-GeBwVar.png
File:VarCont-GBRvsYRI-BwVar.png
File:VarCont-GBRvsYRI-GeBwVar.png
File:VarCont-GBRvsYRI-geneDiff-GeBwVar.png
File:VarCont-YRIcomp-BwVar.png
File:VarCont-YRIcomp-GeBw1.png
File:VarCont-YRIcomp-GeBw5.png
File:VarCont-YRIcomp-GeBwVar.png
File:VarCont-YRIcomp-pv.png
File:Wieland RNA editing 18 10 2012.pdf
Genetic variation data
Geneva April 2012
Genotype quality
Geuvadis browser
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